Nothing
"gap.inspect" <-
function(x) {
# Report the number of gaps, ("-",".",NA), per
# row (i.e. seq) and col (i.e. position) in a
# given "alignment" 'x'
if(is.vector(x)) {
gaps <- is.gap(x)
inds <- which(gaps)
f.inds <- which(!gaps)
gap.pos <- as.numeric(gaps)
gap.col <- gap.pos
gap.row <- sum(gaps)
} else {
if(is.list(x)) {
if(inherits(x, "pdbs")) {
x <- x$xyz; warning("Taking $xyz component (NOT $ali for which you should use 'gap.inspect(x$ali)')")
} else {
x <- x$ali
}
}
gap.pos1 <-( as.numeric(x=="-") + as.numeric(x==".") )
gap.pos2 <- as.numeric(is.na(gap.pos1))
gap.pos<-matrix( colSums(rbind(gap.pos1,gap.pos2), na.rm=TRUE),
ncol=ncol(x))
gap.col <- colSums(gap.pos)
gap.row <- rowSums(gap.pos)
inds <- which(gap.col!=0)
##f.inds=(1:ncol(x))[-inds]
f.inds <- which(gap.col == 0)
}
output=list(t.inds=inds, f.inds=f.inds,
row=gap.row, col=gap.col, bin=gap.pos)
}
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